Phylogenetics
An unrooted tree diagram (a network) makes no assumption about the ancestral line, and does not show the origin or "root" of the taxa in question or the direction of inferred evolutionary transformations.
[6] In the field of cancer research, phylogenetics can be used to study the clonal evolution of tumors and molecular chronology, predicting and showing how cell populations vary throughout the progression of the disease and during treatment, using whole genome sequencing techniques.
[12] With the emergence of biochemistry, organism classifications are now usually based on phylogenetic data, and many systematists contend that only monophyletic taxa should be recognized as named groups.
[13] The degree to which classification depends on inferred evolutionary history differs depending on the school of taxonomy: phenetics ignores phylogenetic speculation altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reflect phylogeny in its classifications by only recognizing groups based on shared, derived characters (synapomorphies); evolutionary taxonomy tries to take into account both the branching pattern and "degree of difference" to find a compromise between them.
[15][16][17] In phylogenetic analysis, taxon sampling selects a small group of taxa to represent the evolutionary history of its broader population.
[19] Unavailable datasets, such as an organism's incomplete DNA and protein amino acid sequences in genomic databases, directly restrict taxonomic sampling.
As seen in the graphic, most of the plotted points are located below the dotted line, which indicates gravitation toward increased accuracy when sampling fewer taxa with more sites per taxon.
[21] It can be traced back to Aristotle, who wrote in his Posterior Analytics, "We may assume the superiority ceteris paribus [other things being equal] of the demonstration which derives from fewer postulates or hypotheses."
Advances in cladistics analysis through faster computer programs and improved molecular techniques have increased the precision of phylogenetic determination, allowing for the identification of species with pharmacological potential.
Historically, phylogenetic screens for pharmacological purposes were used in a basic manner, such as studying the Apocynaceae family of plants, which includes alkaloid-producing species like Catharanthus, known for producing vincristine, an antileukemia drug.
Emerging imagery systems and new analysis techniques allow for the discovery of more genetic relationships in biodiverse fields, which can aid in conservation efforts by identifying rare species that could benefit ecosystems globally.
Whole-genome sequence data from outbreaks or epidemics of infectious diseases can provide important insights into transmission dynamics and inform public health strategies.
However, recent research has explored deducing transmission patterns solely from genomic data using phylodynamics, which involves analyzing the properties of pathogen phylogenies.
[87] The structure of the host contact network significantly impacts the dynamics of outbreaks, and management strategies rely on understanding these transmission patterns.
Researchers have analyzed the structural characteristics of phylogenetic trees generated from simulated bacterial genome evolution across multiple types of contact networks.
By examining simple topological properties of these trees, researchers can classify them into chain-like, homogeneous, or super-spreading dynamics, revealing transmission patterns.
To determine whether tree shapes captured information about underlying disease transmission patterns, researchers simulated the evolution of a bacterial genome over three types of outbreak contact networks—homogeneous, super-spreading, and chain-like.
Figures 2 and 3 illustrate the distributions of these metrics across the three types of outbreaks, revealing clear differences in tree topology depending on the underlying host contact network.
These plots can help identify trends and patterns, such as whether the spread of the pathogen is increasing or decreasing over time, and can highlight potential transmission routes or super-spreader events.
[87] Phylogenetic tools and representations (trees and networks) can also be applied to philology, the study of the evolution of oral languages and written text and manuscripts, such as in the field of quantitative comparative linguistics.
[93] Phylogenetics has been applied to archaeological artefacts such as the early hominin hand-axes,[94] late Palaeolithic figurines,[95] Neolithic stone arrowheads,[96] Bronze Age ceramics,[97] and historical-period houses.
[98] Bayesian methods have also been employed by archaeologists in an attempt to quantify uncertainty in the tree topology and divergence times of stone projectile point shapes in the European Final Palaeolithic and earliest Mesolithic.
